olink_one_non_parametric_posthoc: Function which performs posthoc test per protein for the...

In OlinkAnalyze: Facilitate Analysis of Proteomic Data from Olink

Function which performs posthoc test per protein for the results from Friedman or Kruskal-Wallis Test.

Description

Performs a posthoc test using rstatix::wilcox_test or FSA::dunnTest with Benjamini-Hochberg p-value adjustment per assay (by OlinkID) for each panel at confidence level 0.95. See olink_one_non_parametric for details of input notation.

The function handles both factor and numerical variables.

Usage

olink_one_non_parametric_posthoc(
  df,
  olinkid_list = NULL,
  variable,
  test = "kruskal",
  verbose = TRUE
)

Arguments

df	NPX data frame in long format with at least protein name (Assay), OlinkID, UniProt, Panel and a factor with at least 3 levels.
olinkid_list	Character vector of OlinkID's on which to perform post hoc analysis. If not specified, all assays in df are used.
variable	Single character value or character array.
test	Single character value indicates running the post hoc test for friedman or kruskal.
verbose	Boolean. Default: True. If information about removed samples, factor conversion and final model formula is to be printed to the console.

Value

Tibble of posthoc tests for specified effect, arranged by ascending adjusted p-values.

Columns include:

• Assay: "character" Protein symbol

• OlinkID: "character" Olink specific ID

• UniProt: "character" UniProt ID

• Panel: "character" Name of Olink Panel

• term: "character" term in model

• contrast: "character" the groups that were compared

• estimate: "numeric" the value of the test statistic with a name describing it

• Adjusted_pval: "numeric" adjusted p-value for the test

• Threshold: "character" if adjusted p-value is significant or not (< 0.05)

Examples

library(dplyr)

# One-way Kruskal-Wallis Test
kruskal_results <- olink_one_non_parametric(df = npx_data1,
                                            variable = "Site")

#Friedman Test
friedman_results <- olink_one_non_parametric(df = npx_data1,
                                            variable = "Time",
                                            subject = "Subject",
                                            dependence = TRUE)

#Posthoc test for the results from Friedman Test
friedman_posthoc_results <- olink_one_non_parametric_posthoc(npx_data1,
                                                            variable = "Time",
                                                            test = "friedman",
                                                            olinkid_list = {friedman_results %>%
                                                              filter(Threshold == 'Significant') %>%
                                                              dplyr::select(OlinkID) %>%
                                                              distinct() %>%
                                                              pull()})

OlinkAnalyze documentation built on Nov. 4, 2023, 1:07 a.m.